Align Homocitrate synthase AksA; EC 2.3.3.14; (R)-homo(2)citrate synthase; EC 2.3.3.-; (R)-homo(3)citrate synthase; EC 2.3.3.- (uncharacterized)
to candidate Echvi_2061 Echvi_2061 Isopropylmalate/homocitrate/citramalate synthases
Query= curated2:Q8TW28 (397 letters) >FitnessBrowser__Cola:Echvi_2061 Length = 504 Score = 210 bits (535), Expect = 6e-59 Identities = 133/381 (34%), Positives = 202/381 (53%), Gaps = 10/381 (2%) Query: 23 DTTLRDGEQTPGVSFTPEQKLEIAHLL-DELGVQQIEAGFPVVSEGERDAVRRIAHEGLN 81 DTTLRDGEQT GVSF P +KL+IA LL +EL V +IE VSEGE + V++I H Sbjct: 2 DTTLRDGEQTSGVSFLPSEKLQIAKLLLEELRVDRIEVASARVSEGELEGVKKITHWAAE 61 Query: 82 ADILCLARTLRG-DVDAALDCDVDG---VITFIATSEL-HLKHKLRMSREEVLERIADTV 136 L L D A++D + V+ + L HL H+L+ + E I + Sbjct: 62 KGYLDCVEVLGFVDTPASVDWLTEAGAKVLNLLTKGSLNHLTHQLKKTPVEHFAAIEKCI 121 Query: 137 EYAKDHGLWVAFSAED---GTRTEFEFLERVYRTAEECGADRVHATDTVGVMIPAAMRLF 193 YA + G+ V ED G R ++ + + RV DT+G++ PA + + Sbjct: 122 HYANEKGISVNVYLEDWSSGMRHSRDYTLELIAFLADQNVKRVMLPDTLGLLKPAEVAEY 181 Query: 194 VAKIREVV-DLPIGVHCHDDFGMAVANSLAAVEAGAQAISTTVNGIGERAGNAALEEVIM 252 V + E ++ H H+D+ ++VAN + A+ G I TTVNG+GERAGNA LE V+ Sbjct: 182 VGLVSEQFPEVHFDFHAHNDYDLSVANVMEAINHGISGIHTTVNGLGERAGNAPLESVVA 241 Query: 253 ALKELYGIDPGFNTEVLAELSRKVSEYSGIDVPPNKAVVGENAFRHESGIHVAAVLEEPR 312 L + + + +S+ V ++SG+ +P NK VVGEN F +GIH ++ Sbjct: 242 TLSDFTTVKLNVQENKIYRISKLVEQFSGLHIPSNKPVVGENVFTQTAGIHADGDNKKNL 301 Query: 313 TYEPIDPKEVGMNRKIVLGKHTGRKAVVAKLEELGVEPEEEIVEEVLKRIKALGDRRVRV 372 + + P+ G RK LGK +G+ ++ L ELG++ E E + +V ++I LGDR+ RV Sbjct: 302 YFNDLLPERFGRTRKYALGKTSGKANILKNLLELGIKLEPEELSKVTQKIIELGDRKERV 361 Query: 373 TDSKLEEIVRNVLESRGDRDD 393 T L I+ +VL++ + D Sbjct: 362 TTEDLPYIISDVLQNNSIKKD 382 Lambda K H 0.317 0.135 0.380 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 417 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 397 Length of database: 504 Length adjustment: 33 Effective length of query: 364 Effective length of database: 471 Effective search space: 171444 Effective search space used: 171444 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory